Matlab Software To Do Analyses as in Marron’s Talks Matlab Available from UNC Site License Download Software: Google “Marron Software”

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Presentation transcript:

Matlab Software To Do Analyses as in Marron’s Talks Matlab Available from UNC Site License Download Software: Google “Marron Software”

Matlab Software Choose

Matlab Software Download.zip File, & Expand to 3 Directories

Matlab Software Put these is Matlab Path

Matlab Software Put these is Matlab Path

Matlab Basics Matlab has Modalities:  Interpreted (Type Commands)  Batch (Run “Script Files”)

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode: For description of a function: >> help [function name]

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab in Interpreted Mode: To Find Functions: >> help [category name] e.g. >> help stats

Matlab Basics Matlab in Interpreted Mode:

Matlab Basics Matlab has Modalities:  Interpreted (Type Commands)  Batch (Run “Script Files”) For Serious Scientific Computing: Always Run Scripts

Matlab Basics Matlab Script File:  Just a List of Matlab Commands  Matlab Executes Them in Order Why Bother (Why Not Just Type Commands)? Reproducibility (Can Find Mistakes & Use Again Much Later)

Matlab Script Files An Example: Recall “Brushing Analysis” of Next Generation Sequencing Data

Simple 1 st View: Curve Overlay (log scale) Functional Data Analysis

Often Useful Population View: PCA Scores Functional Data Analysis

Suggestion Of Clusters ??? Functional Data Analysis

Suggestion Of Clusters Which Are These? Functional Data Analysis

Manually “Brush” Clusters Functional Data Analysis

Manually Brush Clusters Clear Alternate Splicing Functional Data Analysis

Matlab Script Files An Example: Recall “Brushing Analysis” of Next Generation Sequencing Data Analysis In Script File: VisualizeNextGen2011.m Matlab Script File Suffix

Matlab Script Files String of Text

Matlab Script Files Command to Display String to Screen

Matlab Script Files Notes About Data (Maximizes Reproducibility)

Matlab Script Files Have Index for Each Part of Analysis

Matlab Script Files So Keep Everything Done (Max’s Reprod’ity)

Matlab Script Files Note Some Are Graphics Shown (Can Repeat)

Matlab Script Files Set Graphics to Default

Matlab Script Files Put Different Program Parts in IF-Block

Matlab Script Files Comment Out Currently Unused Commands

Matlab Script Files Read Data from Excel File

Matlab Script Files For Generic Functional Data Analysis:

Matlab Script Files Input Data Matrix

Matlab Script Files Structure, with Other Settings

Matlab Script Files Make Scores Scatterplot

Matlab Script Files Uses Careful Choice of Color Matrix

Matlab Script Files Start with PCA

Matlab Script Files Then Create Color Matrix

Matlab Script Files Black Red Blue

Matlab Script Files Run Script Using Filename as a Command